What Is a PDB File?

How to open, edit, and convert PDB files

Screenshot of several PDB files in Windows 10 that open with Notepad
PDB Files.

A file with the PDB file extension is most likely a file created in the Program Database format that's used to hold debugging information about a program or module, like a DLL or EXE file. They're sometimes called symbol files.

PDB files map various components and statements in a source code to its final compiled product, which the debugger can then use to find the source file and the location in the executable at which it should stop the debugging process.

Some PDB files might instead be in the Protein Data Bank file format. These PDB files are plain text files that store coordinates regarding protein structures.

Other PDB files are probably created in the Palm Database or PalmDOC file format and used with the PalmOS mobile operating system. Some files in this format use the .PRC file extension instead.

How to Open a PDB File

Different programs use their own PDB file to store data in some sort of structured database format, so each application is used to open its own type of PDB file. Geneious, Intuit Quicken, Microsoft Visual Studio, and Pegasus are just a few examples of programs that might use a PDB file as a database file. Radare and PDBparse might work for opening PDB files too.

Some PDB files are stored as plain text, like Geneious' Program Debug Database files, and are completely human-readable if opened in a text editor. You can open this kind of PDB file with any program that can read text documents, like the built-in Notepad program in Windows. Some other PDB file viewers and editors include Notepad++ and Brackets.

Other PDB database files are not text documents and are only useful when opened with the program that it's intended for. For example, if your PDB file is related in some way to Quicken, then try using that software to view or edit the PDB file. Visual Studio expects to see a PDB file in the same folder as the DLL or EXE file.

You can view and edit PDB files that are Protein Data Bank files, in Windows, Linux, and macOS with Avogadro. Jmol, RasMol, QuickPDB, and USCF Chimera can open a PDB file too. Since these files are plain text, you can open the PDB file in a text editor too.

Palm Desktop should be able to open PDB files that are in the Palm Database file format but you might have to first rename it to have the .PRC file extension for that program to recognize it. To open a PalmDOC PDB file, try STDU Viewer.

How to Convert a PDB File

Program Database files can most likely not be converted to a different file format, at least not with a regular file converter tool. Instead, if there is any tool that can convert this kind of PDB file, it'd be the same program that can open it.

For example, if you need to convert your PDB database file from Quicken, try using that program to do it. This type of conversion, however, is probably not only of little use but also not supported in these database applications (i.e. you probably don't need to convert this kind of PDB file to any other format).

Protein Data Bank files can be converted to other formats with MeshLab. To do this, you might have to first convert the PDB file to WRL with PyMOL from the File > Save Image As > VRML menu, and then import the WRL file in MeshLab and use the File > Export Mesh As menu to ultimately convert the PDB file to STL or another file format.

If you don't need the model to be in color, you can export the PDB file directly to STL with USCF Chimera (the download link is above). Otherwise, you can use the same method as above (with MeshLab) to convert PDB to WRL with USCF Chimera and then export the WRL file to STL with MeshLab.

To convert PDB to PDF or EPUB, if you have a PalmDOC file, is possible a number of ways but the easiest is probably to use an online PDB converter like Zamzar. You can upload your PDB file to that website to have the option of converting it to those formats as well as to AZW3, FB2, MOBI, PML, PRC, TXT, and other eBook file formats.

To convert the PDB file to the FASTA format can be done with Meiler Lab's online PDB to FASTA converter.

It's also possible to convert PDB to CIF (Crystallographic Information format) online using PDBx/mmCIF.

Advanced Reading on PDB Files

You can read a lot more about Program Database files from Microsoft, GitHub, and Wintellect.

There's more to learn about Protein Data Bank files too; see Worldwide Protein Data Bank and RCSB PDB.

Is Your File Still Not Opening?

PDB files that aren't opening with any of the tools from above, probably aren't actually PDB files. What might be happening is that you're misreading the file extension; some file formats use a suffix that closely resembles ".PDB" when they're really unrelated and don't work the same.

For example, a PDF file is a document file but most of the programs from above will not render the text and/or images correctly if you try to open one with these software programs. The same is true for other files with similarly spelled file extensions, like PD, PDE, PDC, and PDO files.

PBD is another that belongs to the EaseUS Todo Backup program and is therefore only useful when opened with that software.

If you don't have a PDB file, then research the file extension that your file does have so that you can find the appropriate program that opens or converts it.

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